Update of the FANTOM web resource: enhancement for studying noncoding genomes Article Swipe
Tomoe Nobusada
,
Chi Wai Yip
,
Saumya Agrawal
,
Jessica Severin
,
Imad Abugessaisa
,
Akira Hasegawa
,
Chung-Chau Hon
,
Soichiro Ide
,
Masaru Koido
,
Atsushi Kondo
,
Hiroshi Masuya
,
Shinya Oki
,
Michihira Tagami
,
Toyoyuki Takada
,
Chikashi Terao
,
Nishad Thalhath
,
Scott Walker
,
Kayoko Yasuzawa
,
Jay W. Shin
,
Michiel de Hoon
,
Piero Carninci
,
Hideya Kawaji
,
Takeya Kasukawa
·
YOU?
·
· 2024
· Open Access
·
· DOI: https://doi.org/10.1093/nar/gkae1047
YOU?
·
· 2024
· Open Access
·
· DOI: https://doi.org/10.1093/nar/gkae1047
The FANTOM web resource (https://fantom.gsc.riken.jp/) has been a unique resource for studying mammalian genomes, which is built on the research activities conducted in the international collaborative project FANTOM (Functional ANnoTation Of the Mammalian genome). In recent updates, we expanded annotations for long non-coding RNAs (lncRNAs) and transcribed cis-regulatory elements (CREs). The former was derived from the large-scale lncRNA perturbations in induced pluripotent stem cells (iPSCs) and integrative analysis of Hi-C data conducted in the sixth iteration of the project (FANTOM6). The resulting annotations of lncRNAs, according to the impact on cellular and molecular phenotypes and the potential RNA-chromatin interactions, are accessible via the interactive ZENBU-Reports framework. The latter involves a new platform, fanta.bio (https://fanta.bio/), which collects transcribed CREs identified via use of an extended dataset of CAGE profiles. The CREs, with their annotations including genetic and epigenetic information, are accessible via a dedicated interface as well as the UCSC Genome Browser Database. These updates offer enhanced opportunities to investigate the functions of non-coding regions within mammalian genomes.
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- Type
- article
- Language
- en
- Landing Page
- https://doi.org/10.1093/nar/gkae1047
- https://academic.oup.com/nar/advance-article-pdf/doi/10.1093/nar/gkae1047/60777621/gkae1047.pdf
- OA Status
- gold
- Cited By
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- Related Works
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- OpenAlex ID
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All OpenAlex metadata
Raw OpenAlex JSON
- OpenAlex ID
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https://openalex.org/W4404733368Canonical identifier for this work in OpenAlex
- DOI
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https://doi.org/10.1093/nar/gkae1047Digital Object Identifier
- Title
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Update of the FANTOM web resource: enhancement for studying noncoding genomesWork title
- Type
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articleOpenAlex work type
- Language
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enPrimary language
- Publication year
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2024Year of publication
- Publication date
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2024-11-27Full publication date if available
- Authors
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Tomoe Nobusada, Chi Wai Yip, Saumya Agrawal, Jessica Severin, Imad Abugessaisa, Akira Hasegawa, Chung-Chau Hon, Soichiro Ide, Masaru Koido, Atsushi Kondo, Hiroshi Masuya, Shinya Oki, Michihira Tagami, Toyoyuki Takada, Chikashi Terao, Nishad Thalhath, Scott Walker, Kayoko Yasuzawa, Jay W. Shin, Michiel de Hoon, Piero Carninci, Hideya Kawaji, Takeya KasukawaList of authors in order
- Landing page
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https://doi.org/10.1093/nar/gkae1047Publisher landing page
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https://academic.oup.com/nar/advance-article-pdf/doi/10.1093/nar/gkae1047/60777621/gkae1047.pdfDirect link to full text PDF
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YesWhether a free full text is available
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goldOpen access status per OpenAlex
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https://academic.oup.com/nar/advance-article-pdf/doi/10.1093/nar/gkae1047/60777621/gkae1047.pdfDirect OA link when available
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Genome browser, Genome, Biology, Chromatin, Computational biology, Resource (disambiguation), Epigenetics, Annotation, Coding (social sciences), Genetics, Bioinformatics, Computer science, Genomics, Gene, Statistics, Mathematics, Computer networkTop concepts (fields/topics) attached by OpenAlex
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5Total citation count in OpenAlex
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2025: 4, 2024: 1Per-year citation counts (last 5 years)
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10Other works algorithmically related by OpenAlex
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